Re: [AMBER] Calculating LJ parameters in Amber format

From: David A Case <>
Date: Thu, 5 May 2016 10:28:20 -0400

On Thu, May 05, 2016, anu chandra wrote:
> I am trying to calculate the LJ parameters, atomic radius and well depth,
> for a divalent metal ion from the A coefficient and B coefficient provided
> in the literature. The A and B coefficient for the ion are follows,
> A = 171.0 , B = 35.0
> Following the methodology described in
> , the calculated values of radius and well depth are, 0.8274 Angstroms and
> 12.8298 kcal/mol respectively.

First, I wonder if you are interpreting the web page correctly? Assuming that
the above parameters have their usual meanings, the minimum distance r*
is (2A/B)^1/6 = 1.462 (remember that Amber uses rmin = r*/2 in its parameter
files) and eps = B^2/4A = 1.79 kcal/mol.

*More importantly*: you must be *very* careful in translating ion parameters
from the literature!. Be sure that the units are in kcal/mol and not kJ/mol.
Be aware that the mixing rules common in the literature may be different than
those Amber uses (remember that your ions will most commonly be interacting
with water molecules, not with other ions.) Ion parameters are very sensitive
to which water model is being chosen.

Amber parameters are available for dozens of divalent ions, and have been
optimized for various water models. Please review carefully the information
in the "Ions" section of the Amber Reference Manual, and consult the papers
referred to there.

....good luck....dac

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Received on Thu May 05 2016 - 07:30:05 PDT
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